Why did the number of crewmen increase further in the last year of the war?

The best estimates are that it was due to the addition of the second 40 mm Bofors gun or possibly because of added electronics or other equipment. However, confirmation of these reasons is hard to find.

We expected to have to invade Japan in order to force a surrender. After what we saw in the Pacific island-hopping campaign, we couldn’t expect Japan to surrender without a desperate, even suicidal, fight. We knew that an invasion would be a very costly undertaking in both men and ships. We expected that the fleet would be harassed constantly by Kamikaze aircraft and suicide boats. Our submarines were likely to be assigned as pickets to warn and help defend the fleet. Therefore, a second 40 mm Bofors was added to many boats. The increased staffing may have been for that gun since five men were likely needed to load and operate it. Fortunately, Japan surrendered after the second atomic bomb was dropped and we no longer needed to invade.

Throughout the war, new equipment was added to the boats to make them more effective. That new gear often needed more operators and maintenance. That was particularly true of the new radars and sonars as well as navigation equipment such as the new LORAN.